Are Comment Codes 003 and 049 Treated Differently?

Effectively, no. The text of each of the comment codes is as follows:

• SAR Comment Code 003 states: "You didn’t report information about your parents because you indicated that you have an unusual circumstance. You need to follow up with your college or career school’s financial aid office before your eligibility for federal student aid can be determined. A financial aid administrator may request documentation of your circumstance in order to complete their review of your FAFSA form." 
• SAR Comment Code 049 states: "You indicated that your parents are unwilling to provide their information on your FAFSA form. Therefore the only federal student aid you may be eligible to receive is a Direct Unsubsidized Loan. The financial aid office at your college or career school may contact you to complete your application. If you want to be considered for other types of federal student aid, you must log in to StudentAid.gov, select 'Make a Correction,'
  and add your parent to your application."

Effective with the 2023-24 award year, schools must reach out to all dependent students who do not provide parental data on the FAFSA (regardless of reason) to inform them about the procedures for requesting a dependency override using professional judgment (PJ), and to collect the necessary documentation.

How you proceed depends on the result of your outreach. If the student indicates provisional independent student status and requests a dependency override (003), refer to AskRegs Knowledgebase Q&A, What Are the Requirements For Implementing Provisional Independent Student Status For 2024-25?

If the student indicates they are not requesting a dependency override and just want a Direct Unsubsidized Loan (049), see AskRegs Q&A, If a Student's Parents Refuse To Provide Support, How Does the Student Complete the FAFSA To Borrow a Direct Unsubsidized Loan?

Reference Dear Colleague Letter GEN-22-15.

Self-Evaluation Checklists: You may consider using NASFAA's Self-Evaluation Checklists, formerly NASFAA's Self-Evaluation Guide, to audit and evaluate your institution's programs related to this topic. It allows administrators to evaluate processes in a centralized, shared, online space. This tool is free for all NASFAA members.